HEADER HYDROLASE INHIBITOR 02-APR-11 3RDY TITLE CRYSTAL STRUCTURE OF BUCKWHEAT TRYPSIN INHIBITOR RBTI AT 1.84 ANGSTROM TITLE 2 RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: BWI-1=PROTEASE INHIBITOR/TRYPSIN INHIBITOR; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTEINASE INHIBITOR; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: FAGOPYRUM ESCULENTUM; SOURCE 3 ORGANISM_COMMON: BUCKWHEAT; SOURCE 4 ORGANISM_TAXID: 3617; SOURCE 5 GENE: BWI-1, EDN1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: M15; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: QIA EXPRESS PQE-31 KEYWDS SERINE PROTEASE INHIBITOR, POTATO INHIBITOR I, TRYPSIN INHIBITOR, KEYWDS 2 TRYPSIN, HYDROLASE INHIBITOR EXPDTA X-RAY DIFFRACTION AUTHOR L.F.WANG,M.LI,W.R.CHANG REVDAT 4 30-OCT-24 3RDY 1 REMARK REVDAT 3 01-NOV-23 3RDY 1 SEQADV REVDAT 2 04-OCT-17 3RDY 1 REMARK REVDAT 1 06-JUL-11 3RDY 0 JRNL AUTH L.F.WANG,F.ZHAO,M.LI,H.ZHANG,Y.GAO,P.CAO,X.PAN,Z.WANG, JRNL AUTH 2 W.R.CHANG JRNL TITL CONFORMATIONAL CHANGES OF RBTI FROM BUCKWHEAT UPON BINDING JRNL TITL 2 TO TRYPSIN: IMPLICATIONS FOR THE ROLE OF THE P(8)' RESIDUE JRNL TITL 3 IN THE POTATO INHIBITOR I FAMILY JRNL REF PLOS ONE V. 6 20950 2011 JRNL REFN ESSN 1932-6203 JRNL PMID 21698291 JRNL DOI 10.1371/JOURNAL.PONE.0020950 REMARK 2 REMARK 2 RESOLUTION. 1.84 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.84 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.46 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 55.1 REMARK 3 NUMBER OF REFLECTIONS : 8344 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.760 REMARK 3 FREE R VALUE TEST SET COUNT : 397 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 14.4640 - 2.6489 0.57 2769 120 0.1929 0.1983 REMARK 3 2 2.6489 - 2.1046 0.54 2596 145 0.1793 0.2223 REMARK 3 3 2.1046 - 1.8391 0.54 2581 132 0.1955 0.2630 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.39 REMARK 3 B_SOL : 64.99 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.010 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.80420 REMARK 3 B22 (A**2) : -5.80420 REMARK 3 B33 (A**2) : -4.37600 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.012 503 REMARK 3 ANGLE : 1.390 685 REMARK 3 CHIRALITY : 0.099 81 REMARK 3 PLANARITY : 0.006 90 REMARK 3 DIHEDRAL : 14.765 181 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3RDY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-APR-11. REMARK 100 THE DEPOSITION ID IS D_1000064812. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-DEC-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BSRF REMARK 200 BEAMLINE : 1W2B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI(111) DOUBLE FLAT-CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR555 FLAT PANEL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8344 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.840 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 24.10 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 46.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.84 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 23.20 REMARK 200 R MERGE FOR SHELL (I) : 0.50000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3RDZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 24% (W/V) PEG MME 2000, 220MM AMMONIUM REMARK 280 SULFATE, 100MM SODIUM ACETATE (PH 4.4), 100MM SODIUM IODIDE, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 22.95300 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 31.32700 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 31.32700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 34.42950 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 31.32700 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 31.32700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 11.47650 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 31.32700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 31.32700 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 34.42950 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 31.32700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 31.32700 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 11.47650 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 22.95300 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -9 REMARK 465 ARG A -8 REMARK 465 GLY A -7 REMARK 465 SER A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 LEU A 1 REMARK 465 ARG A 2 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 3 CG CD OE1 NE2 REMARK 470 GLU A 16 CD OE1 OE2 REMARK 470 ARG A 17 CD NE CZ NH1 NH2 REMARK 470 LYS A 23 CG CD CE NZ REMARK 470 GLU A 30 CD OE1 OE2 REMARK 470 ARG A 45 NE CZ NH1 NH2 REMARK 470 GLU A 58 CD OE1 OE2 REMARK 470 ARG A 59 NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 33 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 33 NE - CZ - NH2 ANGL. DEV. = -4.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ARG A 45 43.27 -92.44 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3RDZ RELATED DB: PDB DBREF 3RDY A 1 69 UNP Q9S9F3 Q9S9F3_FAGES 1 69 SEQADV 3RDY MET A -9 UNP Q9S9F3 EXPRESSION TAG SEQADV 3RDY ARG A -8 UNP Q9S9F3 EXPRESSION TAG SEQADV 3RDY GLY A -7 UNP Q9S9F3 EXPRESSION TAG SEQADV 3RDY SER A -6 UNP Q9S9F3 EXPRESSION TAG SEQADV 3RDY HIS A -5 UNP Q9S9F3 EXPRESSION TAG SEQADV 3RDY HIS A -4 UNP Q9S9F3 EXPRESSION TAG SEQADV 3RDY HIS A -3 UNP Q9S9F3 EXPRESSION TAG SEQADV 3RDY HIS A -2 UNP Q9S9F3 EXPRESSION TAG SEQADV 3RDY HIS A -1 UNP Q9S9F3 EXPRESSION TAG SEQADV 3RDY HIS A 0 UNP Q9S9F3 EXPRESSION TAG SEQRES 1 A 79 MET ARG GLY SER HIS HIS HIS HIS HIS HIS LEU ARG GLN SEQRES 2 A 79 CYS SER GLY LYS GLN GLU TRP PRO GLU LEU VAL GLY GLU SEQRES 3 A 79 ARG GLY SER LYS ALA ALA LYS ILE ILE GLU ASN GLU ASN SEQRES 4 A 79 GLU ASP VAL ARG ALA ILE VAL LEU PRO GLU GLY SER ALA SEQRES 5 A 79 VAL PRO ARG ASP LEU ARG CYS ASP ARG VAL TRP VAL PHE SEQRES 6 A 79 VAL ASP GLU ARG GLY VAL VAL VAL ASP THR PRO VAL VAL SEQRES 7 A 79 MET FORMUL 2 HOH *92(H2 O) HELIX 1 1 TRP A 10 VAL A 14 5 5 HELIX 2 2 ARG A 17 ASN A 29 1 13 SHEET 1 A 2 ARG A 33 PRO A 38 0 SHEET 2 A 2 ARG A 51 VAL A 56 1 O VAL A 54 N ILE A 35 SSBOND 1 CYS A 4 CYS A 49 1555 1555 2.08 CRYST1 62.654 62.654 45.906 90.00 90.00 90.00 P 43 21 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.015961 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015961 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021784 0.00000